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- PDB-4ip1: C-terminal domain of the thiol:disulfide interchange protein DsbD... -

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Basic information

Entry
Database: PDB / ID: 4ip1
TitleC-terminal domain of the thiol:disulfide interchange protein DsbD, Q488K mutant
ComponentsThiol:disulfide interchange protein DsbD
KeywordsOXIDOREDUCTASE / thioredoxin / thiol:disulfide oxidoreductase / bacterial periplasm
Function / homology
Function and homology information


protein-disulfide reductase / protein-disulfide reductase (NAD(P)H) activity / cytochrome complex assembly / response to copper ion / protein-disulfide reductase activity / cell redox homeostasis / electron transfer activity / plasma membrane
Similarity search - Function
Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / Thioredoxin-like / Thiol:disulphide interchange protein DsbD / DsbD gamma / Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulfide interchange protein DsbD, N-terminal / Cytochrome C biogenesis protein, transmembrane domain / Cytochrome C biogenesis protein transmembrane region / Thioredoxin-like domain / Thioredoxin-like fold ...Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / Thioredoxin-like / Thiol:disulphide interchange protein DsbD / DsbD gamma / Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulfide interchange protein DsbD, N-terminal / Cytochrome C biogenesis protein, transmembrane domain / Cytochrome C biogenesis protein transmembrane region / Thioredoxin-like domain / Thioredoxin-like fold / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsSaridakis, E. / Mavridou, D.A.I. / Redfield, C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: An Extended Active-site Motif Controls the Reactivity of the Thioredoxin Fold.
Authors: Mavridou, D.A. / Saridakis, E. / Kritsiligkou, P. / Mozley, E.C. / Ferguson, S.J. / Redfield, C.
History
DepositionJan 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein DsbD


Theoretical massNumber of molelcules
Total (without water)14,6311
Polymers14,6311
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.107, 51.530, 85.039
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thiol:disulfide interchange protein DsbD / Thiol:disulfide exchange protein DsbD / C-type cytochrome biogenesis protein CycZ / Inner membrane ...Thiol:disulfide exchange protein DsbD / C-type cytochrome biogenesis protein CycZ / Inner membrane copper tolerance protein / Protein-disulfide reductase / Disulfide reductase


Mass: 14630.577 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 444-565) / Mutation: Q488K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dsbD, cutA2, cycZ, dipZ, b4136, JW5734 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36655, protein-disulfide reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 21 mg/mL protein, 20% PEG4000, 0.1 M sodium citrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 4, 2012 / Details: mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.47→100 Å / Num. all: 5954 / Num. obs: 5345 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 9.1
Reflection shellResolution: 2.47→2.56 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1.98 / % possible all: 70

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FWF

2fwf


Resolution: 2.47→29.013 Å / SU ML: 2.04 / σ(F): 0.07 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 230 4.57 %RANDOM
Rwork0.1934 ---
obs0.1962 5032 85.09 %-
all-5917 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.236 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5646 Å2-0 Å2-0 Å2
2---0.8974 Å20 Å2
3----1.4659 Å2
Refinement stepCycle: LAST / Resolution: 2.47→29.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 0 118 1062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003963
X-RAY DIFFRACTIONf_angle_d0.6591306
X-RAY DIFFRACTIONf_dihedral_angle_d14.737347
X-RAY DIFFRACTIONf_chiral_restr0.043151
X-RAY DIFFRACTIONf_plane_restr0.002171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-3.11180.3225960.23032218X-RAY DIFFRACTION80
3.1118-29.01540.21881340.17272584X-RAY DIFFRACTION90

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